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- PDB-6apn: HLA-A*0201 single chain trimer with HPV.16 E7 peptide LLMGTLGIV -

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Basic information

Entry
Database: PDB / ID: 6apn
TitleHLA-A*0201 single chain trimer with HPV.16 E7 peptide LLMGTLGIV
ComponentsBeta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera
KeywordsIMMUNE SYSTEM / HLA class I / HLA-A*02 / HPV
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated suppression of host cGAS-STING signal transduction / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host cell cycle progression / symbiont-mediated suppression of host apoptosis / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated suppression of host cGAS-STING signal transduction / symbiont-mediated perturbation of host transcription / symbiont-mediated perturbation of host cell cycle progression / symbiont-mediated suppression of host apoptosis / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / positive regulation of actin filament polymerization / endoplasmic reticulum exit site / cadmium ion binding / TAP binding / protection from natural killer cell mediated cytotoxicity / viral process / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / detection of bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / DNA-binding transcription factor binding / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / immune response / defense response to Gram-positive bacterium / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA-binding transcription factor activity / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / protein domain specific binding / signaling receptor binding
Similarity search - Function
Papillomavirus E7 / E7 protein, Early protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : ...Papillomavirus E7 / E7 protein, Early protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / Protein E7 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsFinton, K.A.K.
CitationJournal: To Be Published
Title: Effects of HLA single chain trimer design on peptide presentation and stability
Authors: Finton, K.A.K.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera
B: Beta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera


Theoretical massNumber of molelcules
Total (without water)100,1822
Polymers100,1822
Non-polymers00
Water3,711206
1
A: Beta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera


Theoretical massNumber of molelcules
Total (without water)50,0911
Polymers50,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera


Theoretical massNumber of molelcules
Total (without water)50,0911
Polymers50,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.363, 65.094, 130.321
Angle α, β, γ (deg.)90.00, 96.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-2-microglobulin--HLA-A*0201--HPV.16 E7 peptide LLMGTLGIV chimera / MHC class I antigen A*2


Mass: 50091.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P, HLA-A, HLAA / Production host: Homo sapiens (human)
References: UniProt: P61769, UniProt: P01892, UniProt: P03129*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailschimera composition: HPV.16 E7 peptide LLMGTLGIV - LINKER -- Beta-2-microglobulin -- LINKER -- HLA- ...chimera composition: HPV.16 E7 peptide LLMGTLGIV - LINKER -- Beta-2-microglobulin -- LINKER -- HLA-A*0201 -- Expression tag

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6,5, 25% PEG 2000 MME

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→50.01 Å / Num. obs: 37686 / % possible obs: 90.7 % / Redundancy: 3.1 % / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MRK

3mrk


Resolution: 2.22→50.01 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.294 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26005 1887 5 %RANDOM
Rwork0.21346 ---
obs0.21582 35786 90.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.033 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20.47 Å2
2---1.42 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.22→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6038 0 0 206 6244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196225
X-RAY DIFFRACTIONr_bond_other_d0.0020.025363
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.928471
X-RAY DIFFRACTIONr_angle_other_deg0.826312372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.465765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33722.961304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77615935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8031548
X-RAY DIFFRACTIONr_chiral_restr0.0720.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021406
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8982.7723071
X-RAY DIFFRACTIONr_mcbond_other0.8972.7713070
X-RAY DIFFRACTIONr_mcangle_it1.584.6643829
X-RAY DIFFRACTIONr_mcangle_other1.584.6653830
X-RAY DIFFRACTIONr_scbond_it0.7552.7533154
X-RAY DIFFRACTIONr_scbond_other0.7552.7543155
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3324.6194640
X-RAY DIFFRACTIONr_long_range_B_refined3.06323.6256685
X-RAY DIFFRACTIONr_long_range_B_other3.03923.5646667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.221→2.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 109 -
Rwork0.27 2174 -
obs--74.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84350.6129-0.45581.7785-0.71471.3830.00820.1292-0.0052-0.0928-0.05990.0218-0.07980.01120.05170.07810.0369-0.03170.1291-0.00030.018319.7452-2.142810.9341
20.6918-0.4346-0.17051.39410.45061.1367-0.00730.1093-0.06410.0295-0.06360.1440.1021-0.17130.07090.0332-0.0252-0.00570.0882-0.01420.021812.8188-12.445524.7726
34.4993-1.91790.46771.3569-0.24931.64820.16590.3381-0.106-0.3014-0.16360.1893-0.1136-0.356-0.00230.18560.066-0.07040.25950.00840.15251.834911.328514.8816
40.5395-0.11840.03551.03890.0060.8760.0115-0.05540.0111-0.0425-0.0148-0.03710.09870.02250.00330.0522-0.0027-0.03740.0794-0.00010.041227.0929-43.713246.6176
51.03690.43880.36521.65720.63161.5328-0.0317-0.09580.04530.0076-0.0905-0.0553-0.01240.08450.12230.05660.0063-0.01270.12420.03990.044837.8796-31.04841.7074
62.68281.64161.93071.93041.70652.29830.0791-0.0325-0.15270.11210.0173-0.23850.10840.2096-0.09630.0889-0.0005-0.05790.15930.01690.118642.7278-20.839352.318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 147
2X-RAY DIFFRACTION2A148 - 368
3X-RAY DIFFRACTION3A371 - 417
4X-RAY DIFFRACTION4B1 - 292
5X-RAY DIFFRACTION5B293 - 364
6X-RAY DIFFRACTION6B365 - 417

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